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Food safety

Better Training for Safer FoodInitiative

Sofia, Bulgaria 6th -8th June 2018

Molecular epidemiology and regional transmission dynamics of

PPR

Arnaud Bataille

Peste des Petits Ruminants (PPR) BTSFThis presentation is delivered under contract with theConsumers, Health, Agriculture and Food Executive Agency(http://ec.europa.eu/chafea). The content of this presentation isthe sole responsibility of Opera S.u.r.l., the IstitutoZooprofilattico Sperimentale Lombardia e Emilia Romagna andthe State Food and Veterinary Service of Latvia and it can in noway be taken to reflect the views of the Consumers, Health,Agriculture and Food Executive Agency or any other body of theEuropean Union. The Consumers, Health, Agriculture and FoodExecutive Agency or any other body of the European Union willnot be responsible under any circumstances for the contents ofcommunication items prepared by the contractors.

Food safety

Molecular epidemiology and regional transmission

dynamics of PPR

Arnaud Bataille

CIRAD, UMR ASTRE, Montpellier, France

OIE/FAO/EU Reference Laboratory for PPR

[email protected]

Food safety

Molecular epidemiology

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▪ PPRV characterised by a high

plasticity of its genome (RNA virus)

▪ Potential to undergo mutations and

evolve quickly

▪ Evolution of the genome results in

different genotypes

▪ Genetic distance can be translated

in relatedness

▪ Provide information on ecology and

virus transmission dynamics

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Molecular epidemiology

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▪ Provide information

on ecology and virus

transmission dynamics

At multiple scales

(within-host, inter-host,

metapopulation,…)

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Phylogenetic studies

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▪ Translation of genetic distance in a

phylogenetic tree

▪ Visualisation of relatedness

between viral strains

▪ With quantification of statistical

support

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▪ Translation of genetic distance in a

phylogenetic tree

▪ Visualisation of relatedness

between viral strains

▪ With quantification of statistical

support

▪ Short N gene sequence (255bp) are

informative

▪ Hundreds of N gene sequences

available on GenBankNP3/NP4

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Information from NP3/NP4 studies:

▪ Identification, spread of genetic lineage

▪ Identification of most closely related

strains with the lineage

▪ Potential origin of emergence

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Example: outbreak in Georgia

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▪ Outbreak of PPR in early 2016

▪ Tushuri sheep in 3 farms near Tbilisi

▪ 451 out of 3,740 animals with symptoms

(11%)

▪ 204 animals (49%) died

Where did it come from?

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Where did it come from?

First hypothesis: neighbouring countries

PPR in Turkey, Iran, Iraq

No information from Armenia or Azerbaijan

Legal or illegal transboundary movements of

animals?

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Phylogenetic study on NP3/NP4 sequences

obtained with 3 samples from Georgia

PPR from Georgia belongs to lineage IV as

expected

But not related to Turkey, Iran, Iraq

Outbreak not due to spread of disease from

Turkey, Iran, Iraq

JQ519922 (Turkey 2010)

JQ388660 (Turkey 2010)

KF478928 (Turkey 2009)

AJ563705 (Turkey 2000)

JX898862 (Iran 2011)

JX898847 (Iran 2010)

JF969755 (Kurdistan 2011)

KF478926 (Turkey 2013)

KF478931 (Turkey 2011)

JQ519949 (Turkey 2011)

KU987610 (Turkey 2015)

KU325493 (Turkey 2015)

KF478927(Turkey 2012)

DQ840198 (Tajikistan 2004)

KJ508833 (Bangladesh 2013)

JF939201 (China 2007)

DQ840181 (Israel 1995)

DQ840184 (Turkey 1996)

DQ840179 (India 1994)

DQ840197 (Saudi Arabia 1998)

KC207867 (Pakistan 2012)

DQ840185 (Iran 1998)

HQ131927 (Morocco 2008)

KP793696 (Algeria 2012)

KJ867541 (Ethiopia 2010)

KX189065 (Egypt 2015)

KX189064 (Egypt 2015)

JX398127 (Eritrea 2011)

KT006588 (Egypt 2014)

JN202923 (Egypt 2010)

HQ131931 (Sudan 2008)

JN202924 (Egypt 2010)

PPRV/Georgia/G1/2016



JX312807 (Egypt 2012)

Lineage IV

Lineage II

Lineage I

Lineage III

Turkish PPR

strains

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Phylogenetic study on NP3/NP4 sequences

obtained with 3 samples from Georgia

Closely related to strains from Egypt, Eritrea,

Sudan

Georgia exports sheep by plane to NE Africa

(Egypt) and Middle East (airport in Tbilisi)

Hypothesis: Infected animal came back with

plane

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▪ Longer nucleotide sequence

provide more information

▪ Genome of 16kb

▪ Can be used for more

complex analyses

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Full genome sequencing

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▪ Classical sanger sequencing

▪ By portions of ~800bp

▪ Long and costly

▪ Some sequencing errors

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Full genome sequencing

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▪ Next generation sequencing

▪ High through-put, large

amount of data generated

▪ Many PPRV genomes

sequenced in one run

▪ Deep sequencing: information

on mutant populations

Over 50 PPRV genomes

sequenced at CIRAD

Illumina sequencing

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Time-dependent phylogenetic studies

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▪ Using historical and recent

samples, with dates

associated to sequences

▪ Evaluation of mutation rate

0.0014 sub/site/year

(human DNA: 10-8 sub/site/year)

▪ Date of emergence of PPRV/

lineage

PPRV: 1904 (1730-1960)

Lineage IV: 1967 (1957-1998)

But not enough historical samples

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Transmission dynamics in endemic regions

▪ PPR transmission and spread linked to livestock trade

▪ Need for better understanding of regional virus transmission dynamics for

efficient control and eradication

▪ Need phylogenetic data to link transboundary transmission with trade

?

Small ruminant market trade network in Mauritania and Senegal

figure: Baron et al. (2016)

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PPRV transmission dynamics in endemic regions

Study in West Africa

Sampling in Senegal (N=41) and neighbouring countries (N=14) in 2010-2014

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Sequencing of 255bp of N gene: 54/55 samples of PPRV-II

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Information from NP3/NP4 studies:

▪ Identification, spread of genetic lineage

▪ Identification of most closely related

strains with the lineage

▪ Potential origin of emergence

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Sequencing of N and H gene (N=41, ~ 5000bp) or complete genome (N=14) for

new PPRV-II samples and historical samples

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PPRV-II phylogeny (N and H genes) in Senegal and neighbours to identify of

transmission clusters

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Study in West Africa: Association with animal trade

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Identical sequences = Direct links between two markets separate by long distance

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Data on animal movement between markets (from veterinary services)

Data on roads, animal density, environmental variables

Which factors explain the distribution of virus (as given by genetic data)?

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Data on animal movement between markets (from veterinary services)

Data on roads, animal density, environmental variables

Which factors explain the distribution of virus (as given by genetic data)?

Modelling shows:

▪ Market community (connected by animal trade) correlates with genetic groups

▪ The more two markets are connected by animal trade, the more closely related

are virus strains sequenced

Strong support for importance of animal trade in virus tranmission dynamics

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PPRV transmission dynamics: conclusion

To understand PPRV transmission and better control disease spread, we

need:

▪ Partial sequence of PPRV strains to follow PPRV distribution and identify origin

of emergence

▪ Genome of historical samples to understand the evolutionary history of PPRV

▪ Genetic data to understand PPRV transboundary transmission dynamics

▪ Complete data on animal trade within country and across borders crucial to

better evaluate risk of spread

▪ Genetic data combined with animal movement data provide better information

than the two type of data separated

Food safety

Better Training for Safer Food

BTSF

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Tel +39 06 96042652- / +39 06 8080111

Fax +39 06 89280678

[email protected]; www.btsftraining.com; www.opera-italy.it

This presentation is delivered under contract with the Consumers, Health, Agriculture and Food Executive Agency (http://ec.europa.eu/chafea). Thecontent of this presentation is the sole responsibility of Opera S.u.r.l., the Istituto Zooprofilattico Sperimentale Lombardia e Emilia Romagna and theState Food and Veterinary Service of Latvia and it can in no way be taken to reflect the views of the Consumers, Health, Agriculture and FoodExecutive Agency or any other body of the European Union. The Consumers, Health, Agriculture and Food Executive Agency or any other body of theEuropean Union will not be responsible under any circumstances for the contents of communication items prepared by the contractors.

• European CommissionConsumers, Health and Food Executive Agency

DRB A3/042L-2920 Luxembourg

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